I really don't think that's what they're saying. It's quite possible many old games may do things that cannot figure out workarounds for. For example, the two most obvious might be leaderboards and matchmaking. Perhaps some of these old games have code that break under the new system. But these aren't Sony's games, not to mention they're long ago printed to plastic. Basically, Sony's just saying that name changes may break older games and they're doing their best to ensure as many work as possible.
Legacy systems are a nightmare, period. Any massive change like this to an ecosystem as large, as old, and as wide spread as PSN would be difficult.